A new investigation into a deadly nighttime collision involving a U.S. Navy destroyer heading toward a secret mission in the South China Sea reveals several warning signs leading up to the tragic accident that took seven sailors' lives.

ProPublica, a nonprofit that produces investigative journalism, published a series of reports this week on the destroyer Fitzgerald's June 2017 collision with a cargo ship off the coast of Japan. Titled "Fight the ship: Death and valor on a warship doomed by its own Navy," the report reveals multiple troubling mistakes made by Navy leaders, some of which were previously undisclosed.

It also details courageous actions and heartbreaking choices from the ship's crew.

ProPublica combed through more than 13,000 pages of investigative records and interviewed scores of Fitzgerald crew members, Navy officers and maritime experts. Here's a look at some of the report's findings:

1. Incomplete certifications.

Even as the destroyer was headed on a secret mission toward contested waters in the South China Sea, the Fitzgerald had not met its readiness requirements.

"The Navy required destroyers to pass 22 certification tests to prove themselves seaworthy and battle-ready before sailing," ProPublica reported. "The Fitzgerald had passed just seven of these tests."

Perhaps most troubling, according to the report, is that the Fitz "was not even qualified to conduct its chief mission, anti-ballistic missile defense."

The destroyer, ProPublica reported, had "maneuvered dangerously close to vessels on at least three occasions." But the incidents had gone mostly unreported. Eric Uhden, a prior-enlisted conning officer responsible for the safe movement of the ship, even told the Fitzgerald's second-in-command, Cmdr. Sean Babbitt, that there was a serious problem on the ship, ProPublica reported.

"And the only way for things to get better here is for us to have a serious accident or someone to die," Uhden added.

3. A ship-wide blackout.

About a week before the collision, there was a fire aboard the Fitzgerald, according to ProPublica. It resulted in a ship-wide blackout, and the classified and unclassified email systems failed.

"Officers used Gmail instead," ProPublica reported.

4. Radar problems.

Reports show that the Fitzgerald's radars weren't in full working order. Sometimes they didn't pick up nearby ships, ProPublica reported. The Fitz relied on a navigation system with 17-year-old software and since the screens didn't automatically update to show the presence of new ships, "a sailor had to punch a button a thousand times an hour" to refresh them, the report states.

Perhaps more disturbing though was the belief that even if the radars had been fully functional, "it's not clear the crew knew how to operate them," ProPublica reported.

5. Ignored pleas.

The Fitzgerald was not the only tragic mishap in the Pacific in 2017. Less than two months later, the destroyer John McCain collided with an oil tanker near Singapore and 10 sailors were killed.

Days after that accident, then-commander of 7th Fleet Vice Adm. Joseph Aucoin was relieved of command. Now, he told ProPublica, he wants "the truth to come out."

Aucoin -- who'd pleaded for more manpower, ships and training time -- told ProPublica that Navy leadership has not taken responsibility for undermining America's sea-fighting ability.

6. Crew dedication.

Despite the ship's problems, the Fitzgerald's crew responded courageously when the worst happened. Leaders helped get as many of their sailors as possible to safety, putting their own lives in danger to assist others. It was the crew's actions, the report states, that kept the Fitz afloat.

"They worked in the dark, without power, without steering, without communications," the story states.

"A young officer scribbled algebraic equations in a notebook to figure out how to right the listing vessel," ProPublica reported. "The crew bailed out the ship with buckets after pumps failed. As the Fitzgerald struggled to return to port, its navigational displays failed and backup batteries ran out. The ship's navigator used a handheld commercial GPS unit and paper charts to guide the ship home."

7. A commander's call.

The day before the collision, Cmdr. Bryce Benson, the ship's former commanding officer, had sailors report to duty at 6 a.m. for training. When the drills didn't wrap up until 11 p.m., Benson made a last-minute switch to his typical night orders.

"Normally, Benson directed the officer of the deck to call him if the ship deviated from its planned course by more than 500 yards to avoid traffic," ProPublica reported. "But this night, Benson doubled the number to 1,000 yards, giving the officer more room to maneuver without having to wake him."

8. Possible confrontations.

One of the reasons Benson needed the rest, according to the report, is because he was concerned about the Fitz's upcoming mission.

Even though it's common for COs to remain on the bridge during busy nighttime transits, Benson was worried about sailing into contested waters with territorial disputes off the coast of China, which, as ProPublica points out, "could result in confrontations with Chinese warships."

That left a junior crew that had also had a long day of training in a challenging situation.

9. The crew was undermanned.

Before that mission, the Fitz had spent several months in the repair yards, and almost half of the crew had turned over, ProPublica reported. The new crew was "younger, less seasoned," the story states.

That was "the highest percentage of new crew members of any destroyer in the fleet," ProPublica reported.

"But naval commanders had skimped even further, cutting into the number of sailors Benson needed to keep the ship running smoothly," the story states. "The Fitzgerald had around 270 people total -- short of the 303 sailors called for by the Navy."

10. Key vacancies.

That left key positions aboard the Fitz unfilled -- despite frequent asks from its leaders to Navy higher-ups, ProPublica reported.

"The senior enlisted quartermaster position -- charged with training inexperienced sailors to steer the ship -- had gone unfilled for more than two years," the report states. "The technician in charge of the ship's radar was on medical leave, with no replacement."

That, they added, "made it difficult to post watches on both the starboard and port sides of the ship, a once-common Navy practice."